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M2 mutant (R111K:Y134F:T54V:R132Q:P39Y:R59Y) of human cellular retinoic acid binding protein II - 1l conjugate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Z2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 281 0.2 M sodium malonate pH 7 and 20% w/v polyethylene glycol 3.350
Crystal Properties Matthews coefficient Solvent content 3.17 61.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.836 α = 90 b = 57.836 β = 90 c = 101.9 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2022-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.953738 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.4 50.09 100 0.078 0.083 0.025 0.998 14.8 10.9 8156 58.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 100 1.107 1.16 0.342 0.915 2.5 11.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.4 44.99 7684 452 99.93 0.20595 0.20123 0.2024 0.28117 0.2814 RANDOM 67.938
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.04 0.02 0.04 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.402 r_dihedral_angle_4_deg 19.224 r_dihedral_angle_3_deg 17.768 r_long_range_B_refined 11.611 r_dihedral_angle_1_deg 8.064 r_scbond_it 7.995 r_mcangle_it 7.994 r_mcbond_it 5.845 r_angle_refined_deg 1.715 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.402 r_dihedral_angle_4_deg 19.224 r_dihedral_angle_3_deg 17.768 r_long_range_B_refined 11.611 r_dihedral_angle_1_deg 8.064 r_scbond_it 7.995 r_mcangle_it 7.994 r_mcbond_it 5.845 r_angle_refined_deg 1.715 r_chiral_restr 0.127 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1043 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing